1
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Jakobsen NA, Turkalj S, Zeng AGX, Stoilova B, Metzner M, Rahmig S, Nagree MS, Shah S, Moore R, Usukhbayar B, Angulo Salazar M, Gafencu GA, Kennedy A, Newman S, Kendrick BJL, Taylor AH, Afinowi-Luitz R, Gundle R, Watkins B, Wheway K, Beazley D, Murison A, Aguilar-Navarro AG, Flores-Figueroa E, Dakin SG, Carr AJ, Nerlov C, Dick JE, Xie SZ, Vyas P. Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging. Cell Stem Cell 2024:S1934-5909(24)00207-8. [PMID: 38917807 DOI: 10.1016/j.stem.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Clonal hematopoiesis (CH) arises when hematopoietic stem cells (HSCs) acquire mutations, most frequently in the DNMT3A and TET2 genes, conferring a competitive advantage through mechanisms that remain unclear. To gain insight into how CH mutations enable gradual clonal expansion, we used single-cell multi-omics with high-fidelity genotyping on human CH bone marrow (BM) samples. Most of the selective advantage of mutant cells occurs within HSCs. DNMT3A- and TET2-mutant clones expand further in early progenitors, while TET2 mutations accelerate myeloid maturation in a dose-dependent manner. Unexpectedly, both mutant and non-mutant HSCs from CH samples are enriched for inflammatory and aging transcriptomic signatures, compared with HSCs from non-CH samples, revealing a non-cell-autonomous effect. However, DNMT3A- and TET2-mutant HSCs have an attenuated inflammatory response relative to wild-type HSCs within the same sample. Our data support a model whereby CH clones are gradually selected because they are resistant to the deleterious impact of inflammation and aging.
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Affiliation(s)
- Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Bilyana Stoilova
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Susann Rahmig
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Murtaza S Nagree
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sayyam Shah
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rachel Moore
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Batchimeg Usukhbayar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mirian Angulo Salazar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Grigore-Aristide Gafencu
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alison Kennedy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Simon Newman
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Benjamin J L Kendrick
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Adrian H Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rasheed Afinowi-Luitz
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Roger Gundle
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Bridget Watkins
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Kim Wheway
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Debra Beazley
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alicia G Aguilar-Navarro
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Eugenia Flores-Figueroa
- Unidad de Investigación Médica en Enfermedades Oncológicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Stephanie G Dakin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Andrew J Carr
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK; Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Claus Nerlov
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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2
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Siebert-Kuss LM, Dietrich V, Di Persio S, Bhaskaran J, Stehling M, Cremers JF, Sandmann S, Varghese J, Kliesch S, Schlatt S, Vaquerizas JM, Neuhaus N, Laurentino S. Genome-wide DNA methylation changes in human spermatogenesis. Am J Hum Genet 2024; 111:1125-1139. [PMID: 38759652 PMCID: PMC11179423 DOI: 10.1016/j.ajhg.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Sperm production and function require the correct establishment of DNA methylation patterns in the germline. Here, we examined the genome-wide DNA methylation changes during human spermatogenesis and its alterations in disturbed spermatogenesis. We found that spermatogenesis is associated with remodeling of the methylome, comprising a global decline in DNA methylation in primary spermatocytes followed by selective remethylation, resulting in a spermatids/sperm-specific methylome. Hypomethylated regions in spermatids/sperm were enriched in specific transcription factor binding sites for DMRT and SOX family members and spermatid-specific genes. Intriguingly, while SINEs displayed differential methylation throughout spermatogenesis, LINEs appeared to be protected from changes in DNA methylation. In disturbed spermatogenesis, germ cells exhibited considerable DNA methylation changes, which were significantly enriched at transposable elements and genes involved in spermatogenesis. We detected hypomethylation in SVA and L1HS in disturbed spermatogenesis, suggesting an association between the abnormal programming of these regions and failure of germ cells progressing beyond meiosis.
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Affiliation(s)
- Lara M Siebert-Kuss
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Verena Dietrich
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Sara Di Persio
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Jahnavi Bhaskaran
- MRC Laboratory of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK; Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Martin Stehling
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Jann-Frederik Cremers
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital of Münster, Münster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital of Münster, Münster, Germany
| | - Stefan Schlatt
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Juan M Vaquerizas
- MRC Laboratory of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK; Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Nina Neuhaus
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, Institute of Reproductive and Regenerative Biology, University of Münster, Münster, Germany.
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3
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Zhang X, Gao X, Liu Z, Shao F, Yu D, Zhao M, Qin X, Wang S. Microbiota regulates the TET1-mediated DNA hydroxymethylation program in innate lymphoid cell differentiation. Nat Commun 2024; 15:4792. [PMID: 38839760 PMCID: PMC11153590 DOI: 10.1038/s41467-024-48794-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
Innate lymphoid cell precursors (ILCPs) develop into distinct subsets of innate lymphoid cells (ILCs) with specific functions. The epigenetic program underlying the differentiation of ILCPs into ILC subsets remains poorly understood. Here, we reveal the genome-wide distribution and dynamics of the DNA methylation and hydroxymethylation in ILC subsets and their respective precursors. Additionally, we find that the DNA hydroxymethyltransferase TET1 suppresses ILC1 but not ILC2 or ILC3 differentiation. TET1 deficiency promotes ILC1 differentiation by inhibiting TGF-β signaling. Throughout ILCP differentiation at postnatal stage, gut microbiota contributes to the downregulation of TET1 level. Microbiota decreases the level of cholic acid in the gut, impairs TET1 expression and suppresses DNA hydroxymethylation, ultimately resulting in an expansion of ILC1s. In adult mice, TET1 suppresses the hyperactivation of ILC1s to maintain intestinal homeostasis. Our findings provide insights into the microbiota-mediated epigenetic programming of ILCs, which links microbiota-DNA methylation crosstalk to ILC differentiation.
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Affiliation(s)
- Xusheng Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xintong Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhen Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fei Shao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dou Yu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Min Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiwen Qin
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Shuo Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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4
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Whiting FJH, Househam J, Baker AM, Sottoriva A, Graham TA. Phenotypic noise and plasticity in cancer evolution. Trends Cell Biol 2024; 34:451-464. [PMID: 37968225 DOI: 10.1016/j.tcb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023]
Abstract
Non-genetic alterations can produce changes in a cell's phenotype. In cancer, these phenomena can influence a cell's fitness by conferring access to heritable, beneficial phenotypes. Herein, we argue that current discussions of 'phenotypic plasticity' in cancer evolution ignore a salient feature of the original definition: namely, that it occurs in response to an environmental change. We suggest 'phenotypic noise' be used to distinguish non-genetic changes in phenotype that occur independently from the environment. We discuss the conceptual and methodological techniques used to identify these phenomena during cancer evolution. We propose that the distinction will guide efforts to define mechanisms of phenotype change, accelerate translational work to manipulate phenotypes through treatment, and, ultimately, improve patient outcomes.
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Affiliation(s)
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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5
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Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nat Commun 2024; 15:4325. [PMID: 38773071 PMCID: PMC11109152 DOI: 10.1038/s41467-024-48508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
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Affiliation(s)
- Giulia Schiroli
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Vinay Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Trine A Kristiansen
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christina Mayerhofer
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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6
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Zhu T, Tong H, Du Z, Beck S, Teschendorff AE. An improved epigenetic counter to track mitotic age in normal and precancerous tissues. Nat Commun 2024; 15:4211. [PMID: 38760334 PMCID: PMC11101651 DOI: 10.1038/s41467-024-48649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
The cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA methylation (DNAm) clocks are promising tools to molecularly track mitotic age, yet their relationship is underexplored and their potential for cancer risk prediction in normal tissues remains to be demonstrated. Here we build and validate an improved pan-tissue DNAm counter of total mitotic age called stemTOC. We demonstrate that stemTOC's mitotic age proxy increases with the tumor cell-of-origin fraction in each of 15 cancer-types, in precancerous lesions, and in normal tissues exposed to major cancer risk factors. Extensive benchmarking against 6 other mitotic counters shows that stemTOC compares favorably, specially in the preinvasive and normal-tissue contexts. By cross-correlating stemTOC to two clock-like somatic mutational signatures, we confirm the mitotic-like nature of only one of these. Our data points towards DNAm as a promising molecular substrate for detecting mitotic-age increases in normal tissues and precancerous lesions, and hence for developing cancer-risk prediction strategies.
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Affiliation(s)
- Tianyu Zhu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Zhaozhen Du
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- Medical Genomics Group, UCL Cancer Institute, University College London, 72 Huntley Street, WC1E 6BT, London, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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7
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Winter S, Götze KS, Hecker JS, Metzeler KH, Guezguez B, Woods K, Medyouf H, Schäffer A, Schmitz M, Wehner R, Glauche I, Roeder I, Rauner M, Hofbauer LC, Platzbecker U. Clonal hematopoiesis and its impact on the aging osteo-hematopoietic niche. Leukemia 2024; 38:936-946. [PMID: 38514772 PMCID: PMC11073997 DOI: 10.1038/s41375-024-02226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Clonal hematopoiesis (CH) defines a premalignant state predominantly found in older persons that increases the risk of developing hematologic malignancies and age-related inflammatory diseases. However, the risk for malignant transformation or non-malignant disorders is variable and difficult to predict, and defining the clinical relevance of specific candidate driver mutations in individual carriers has proved to be challenging. In addition to the cell-intrinsic mechanisms, mutant cells rely on and alter cell-extrinsic factors from the bone marrow (BM) niche, which complicates the prediction of a mutant cell's fate in a shifting pre-malignant microenvironment. Therefore, identifying the insidious and potentially broad impact of driver mutations on supportive niches and immune function in CH aims to understand the subtle differences that enable driver mutations to yield different clinical outcomes. Here, we review the changes in the aging BM niche and the emerging evidence supporting the concept that CH can progressively alter components of the local BM microenvironment. These alterations may have profound implications for the functionality of the osteo-hematopoietic niche and overall bone health, consequently fostering a conducive environment for the continued development and progression of CH. We also provide an overview of the latest technology developments to study the spatiotemporal dependencies in the CH BM niche, ideally in the context of longitudinal studies following CH over time. Finally, we discuss aspects of CH carrier management in clinical practice, based on work from our group and others.
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Affiliation(s)
- Susann Winter
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Katharina S Götze
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine III, Technical University of Munich (TUM), School of Medicine and Health, Munich, Germany
- German MDS Study Group (D-MDS), Leipzig, Germany
| | - Judith S Hecker
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine III, Technical University of Munich (TUM), School of Medicine and Health, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich (TUM), Munich, Germany
| | - Klaus H Metzeler
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology, Cellular Therapy, Hemostaseology and Infectious Disease, University of Leipzig Medical Center, Leipzig, Germany
| | - Borhane Guezguez
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Oncology, University Medical Center Mainz, Mainz, Germany
| | - Kevin Woods
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Oncology, University Medical Center Mainz, Mainz, Germany
| | - Hind Medyouf
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Frankfurt am Main, Germany
| | - Alexander Schäffer
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Marc Schmitz
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Rebekka Wehner
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Ingo Roeder
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martina Rauner
- Division of Endocrinology, Diabetes and Bone Diseases, Department of Medicine III, and Center for Healthy Aging, University Medical Center, TU Dresden, Dresden, Germany
| | - Lorenz C Hofbauer
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Division of Endocrinology, Diabetes and Bone Diseases, Department of Medicine III, and Center for Healthy Aging, University Medical Center, TU Dresden, Dresden, Germany.
| | - Uwe Platzbecker
- German Cancer Consortium (DKTK), CHOICE Consortium, Partner Sites Dresden/Munich/Frankfurt/Mainz, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German MDS Study Group (D-MDS), Leipzig, Germany.
- Department of Hematology, Cellular Therapy, Hemostaseology and Infectious Disease, University of Leipzig Medical Center, Leipzig, Germany.
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8
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Izzo F, Myers RM, Ganesan S, Mekerishvili L, Kottapalli S, Prieto T, Eton EO, Botella T, Dunbar AJ, Bowman RL, Sotelo J, Potenski C, Mimitou EP, Stahl M, El Ghaity-Beckley S, Arandela J, Raviram R, Choi DC, Hoffman R, Chaligné R, Abdel-Wahab O, Smibert P, Ghobrial IM, Scandura JM, Marcellino B, Levine RL, Landau DA. Mapping genotypes to chromatin accessibility profiles in single cells. Nature 2024; 629:1149-1157. [PMID: 38720070 PMCID: PMC11139586 DOI: 10.1038/s41586-024-07388-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 04/04/2024] [Indexed: 05/19/2024]
Abstract
In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates1-3. Therefore, somatic mutations are likely to alter chromatin accessibility patterns, as they disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wild-type cells. Here, to chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed genotyping of targeted loci with single-cell chromatin accessibility (GoT-ChA). This high-throughput platform links genotypes to chromatin accessibility at single-cell resolution across thousands of cells within a single assay. We applied GoT-ChA to CD34+ cells from patients with myeloproliferative neoplasms with JAK2V617F-mutated haematopoiesis. Differential accessibility analysis between wild-type and JAK2V617F-mutant progenitors revealed both cell-intrinsic and cell-state-specific shifts within mutant haematopoietic precursors, including cell-intrinsic pro-inflammatory signatures in haematopoietic stem cells, and a distinct profibrotic inflammatory chromatin landscape in megakaryocytic progenitors. Integration of mitochondrial genome profiling and cell-surface protein expression measurement allowed expansion of genotyping onto DOGMA-seq through imputation, enabling single-cell capture of genotypes, chromatin accessibility, RNA expression and cell-surface protein expression. Collectively, we show that the JAK2V617F mutation leads to epigenetic rewiring in a cell-intrinsic and cell type-specific manner, influencing inflammation states and differentiation trajectories. We envision that GoT-ChA will empower broad future investigations of the critical link between somatic mutations and epigenetic alterations across clonal populations in malignant and non-malignant contexts.
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Affiliation(s)
- Franco Izzo
- New York Genome Center, New York, NY, USA.
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Saravanan Ganesan
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Levan Mekerishvili
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Sanjay Kottapalli
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Tamara Prieto
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Elliot O Eton
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theo Botella
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Andrew J Dunbar
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L Bowman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesus Sotelo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Catherine Potenski
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Eleni P Mimitou
- New York Genome Center, New York, NY, USA
- Immunai, New York, NY, USA
| | - Maximilian Stahl
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Oncology, Division of Leukemia, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sebastian El Ghaity-Beckley
- Division of Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - JoAnn Arandela
- Division of Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ramya Raviram
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Daniel C Choi
- Laboratory of Molecular Hematopoiesis, Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Richard T. Silver MD Myeloproliferative Neoplasm Center, Weill Cornell Medicine, New York, NY, USA
- Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ronald Hoffman
- Division of Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ronan Chaligné
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- SAIL: Single-cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter Smibert
- New York Genome Center, New York, NY, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Irene M Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joseph M Scandura
- Laboratory of Molecular Hematopoiesis, Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Richard T. Silver MD Myeloproliferative Neoplasm Center, Weill Cornell Medicine, New York, NY, USA
- Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bridget Marcellino
- Division of Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ross L Levine
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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9
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Yang C, Yokomori R, Chua LH, Tan SH, Koh MY, Totani H, Sanda T, Suda T. Deciphering the regulatory landscape of murine splenic response to anemic stress at single-cell resolution. Blood Adv 2024; 8:1651-1666. [PMID: 38315834 PMCID: PMC11006810 DOI: 10.1182/bloodadvances.2023011965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/07/2024] Open
Abstract
ABSTRACT Stress erythropoiesis can be influenced by multiple mediators through both intrinsic and extrinsic mechanisms in early erythroid precursors. Single-cell RNA sequencing was conducted on spleen tissue isolated from mice subjected to phenylhydrazine and serial bleeding to explore novel molecular mechanisms of stress erythropoiesis. Our results showed prominent emergence of early erythroblast populations under both modes of anemic stress. Analysis of gene expression revealed distinct phases during the development of emerging erythroid cells. Interestingly, we observed the presence of a "hiatus" subpopulation characterized by relatively low level of transcriptional activities that transitions between early stages of emerging erythroid cells, with moderate protein synthesis activities. Moreover, single-cell analysis conducted on macrophage populations revealed distinct transcriptional programs in Vcam1+ macrophages under stress. Notably, a novel marker, CD81, was identified for labeling central macrophages in erythroblastic islands (EBIs), which is functionally required for EBIs to combat anemic stress. These findings offer fresh insights into the intrinsic and extrinsic pathways of early erythroblasts' response to stress, potentially informing the development of innovative therapeutic approaches for addressing anemic-related conditions.
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Affiliation(s)
- Chong Yang
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Rui Yokomori
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lee Hui Chua
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mun Yee Koh
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Haruhito Totani
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Toshio Suda
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- International Research Centre for Medical Sciences, Kumamoto University, Kumamoto, Japan
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10
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Scherer M, Singh I, Braun M, Szu-Tu C, Kardorff M, Rühle J, Frömel R, Beneyto-Calabuig S, Raffel S, Rodriguez-Fraticelli A, Velten L. Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587514. [PMID: 38617287 PMCID: PMC11014487 DOI: 10.1101/2024.04.01.587514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Current approaches to lineage tracing of stem cell clones require genetic engineering or rely on sparse somatic DNA variants, which are difficult to capture at single-cell resolution. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a droplet-based method for transgene-free lineage tracing, and apply it to study hematopoiesis, capturing hundreds of clonal trajectories across almost 100,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation. Applied to unperturbed hematopoiesis, we describe an overall decline of clonal complexity during murine ageing and the expansion of rare low-output stem cell clones. In aged human donors, we identified expanded hematopoietic clones with and without genetic lesions, and various degrees of clonal complexity. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing at scale.
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Affiliation(s)
- Michael Scherer
- Computational Biology and Health Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Indranil Singh
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Martina Braun
- Computational Biology and Health Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Chelsea Szu-Tu
- Computational Biology and Health Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Michael Kardorff
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Julia Rühle
- Computational Biology and Health Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Robert Frömel
- Computational Biology and Health Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sergi Beneyto-Calabuig
- Computational Biology and Health Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Raffel
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Alejo Rodriguez-Fraticelli
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Lars Velten
- Computational Biology and Health Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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11
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He L, Cao Y, Sun L. NSD family proteins: Rising stars as therapeutic targets. CELL INSIGHT 2024; 3:100151. [PMID: 38371593 PMCID: PMC10869250 DOI: 10.1016/j.cellin.2024.100151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Epigenetic modifications, including DNA methylation and histone post-translational modifications, intricately regulate gene expression patterns by influencing DNA accessibility and chromatin structure in higher organisms. These modifications are heritable, are independent of primary DNA sequences, undergo dynamic changes during development and differentiation, and are frequently disrupted in human diseases. The reversibility of epigenetic modifications makes them promising targets for therapeutic intervention and drugs targeting epigenetic regulators (e.g., tazemetostat, targeting the H3K27 methyltransferase EZH2) have been applied in clinical therapy for multiple cancers. The NSD family of H3K36 methyltransferase enzymes-including NSD1 (KMT3B), NSD2 (MMSET/WHSC1), and NSD3 (WHSC1L1)-are now receiving drug development attention, with the exciting advent of an NSD2 inhibitor (KTX-1001) advancing to Phase I clinical trials for relapsed or refractory multiple myeloma. NSD proteins recognize and catalyze methylation of histone lysine marks, thereby regulating chromatin integrity and gene expression. Multiple studies have implicated NSD proteins in human disease, noting impacts from translocations, aberrant expression, and various dysfunctional somatic mutations. Here, we review the biological functions of NSD proteins, epigenetic cooperation related to NSD proteins, and the accumulating evidence linking these proteins to developmental disorders and tumorigenesis, while additionally considering prospects for the development of innovative epigenetic therapies.
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Affiliation(s)
- Lin He
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Yiping Cao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
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12
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Zhu L, Wang J. Quantifying Landscape-Flux via Single-Cell Transcriptomics Uncovers the Underlying Mechanism of Cell Cycle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308879. [PMID: 38353329 DOI: 10.1002/advs.202308879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/23/2024] [Indexed: 04/25/2024]
Abstract
Recent developments in single-cell sequencing technology enable the acquisition of entire transcriptome data. Understanding the underlying mechanism and identifying the driving force of transcriptional regulation governing cell function directly from these data remains challenging. This study reconstructs a continuous vector field of the cell cycle based on discrete single-cell RNA velocity to quantify the single-cell global nonequilibrium dynamic landscape-flux. It reveals that large fluctuations disrupt the global landscape and genetic perturbations alter landscape-flux, thus identifying key genes in maintaining cell cycle dynamics and predicting associated functional effects. Additionally, it quantifies the fundamental energy cost of the cell cycle initiation and unveils that sustaining the cell cycle requires curl flux and dissipation to maintain the oscillatory phase coherence. This study enables the inference of the cell cycle gene regulatory networks directly from the single-cell transcriptomic data, including the feedback mechanisms and interaction intensity. This provides a golden opportunity to experimentally verify the landscape-flux theory and also obtain its associated quantifications. It also offers a unique framework for combining the landscape-flux theory and single-cell high-through sequencing experiments for understanding the underlying mechanisms of the cell cycle and can be extended to other nonequilibrium biological processes, such as differentiation development and disease pathogenesis.
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Affiliation(s)
- Ligang Zhu
- College of Physics, Jilin University, Changchun, 130021, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Jin Wang
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325001, P. R. China
- Department of Chemistry, Physics and Astronomy, Stony Brook University, Stony Brook, NY, 11794, USA
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13
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Yu Z, Coorens THH, Uddin MM, Ardlie KG, Lennon N, Natarajan P. Genetic variation across and within individuals. Nat Rev Genet 2024:10.1038/s41576-024-00709-x. [PMID: 38548833 DOI: 10.1038/s41576-024-00709-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2024] [Indexed: 04/12/2024]
Abstract
Germline variation and somatic mutation are intricately connected and together shape human traits and disease risks. Germline variants are present from conception, but they vary between individuals and accumulate over generations. By contrast, somatic mutations accumulate throughout life in a mosaic manner within an individual due to intrinsic and extrinsic sources of mutations and selection pressures acting on cells. Recent advancements, such as improved detection methods and increased resources for association studies, have drastically expanded our ability to investigate germline and somatic genetic variation and compare underlying mutational processes. A better understanding of the similarities and differences in the types, rates and patterns of germline and somatic variants, as well as their interplay, will help elucidate the mechanisms underlying their distinct yet interlinked roles in human health and biology.
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Affiliation(s)
- Zhi Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Md Mesbah Uddin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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14
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Hosseini M, Voisin V, Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu AC, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D’Alessandro A, Young K, Wu Y, Fiumara M, Ferrari S, Naldini L, Gaiti F, Pai S, Schimmer AD, Bader GD, Dick JE, Xie SZ, Trowbridge JJ, Chan SM. Metformin reduces the clonal fitness of Dnmt3aR878H hematopoietic stem and progenitor cells by reversing their aberrant metabolic and epigenetic state. RESEARCH SQUARE 2024:rs.3.rs-3874821. [PMID: 38405837 PMCID: PMC10889081 DOI: 10.21203/rs.3.rs-3874821/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Clonal hematopoiesis (CH) arises when a hematopoietic stem cell (HSC) acquires a mutation that confers a competitive advantage over wild-type (WT) HSCs, resulting in its clonal expansion. Individuals with CH are at an increased risk of developing hematologic neoplasms and a range of age-related inflammatory illnesses1-3. Therapeutic interventions that suppress the expansion of mutant HSCs have the potential to prevent these CH-related illnesses; however, such interventions have not yet been identified. The most common CH driver mutations are in the DNA methyltransferase 3 alpha (DNMT3A) gene with arginine 882 (R882) being a mutation hotspot. Here we show that murine hematopoietic stem and progenitor cells (HSPCs) carrying the Dnmt3aR878H/+ mutation, which is equivalent to human DNMT3AR882H/+, have increased mitochondrial respiration compared with WT cells and are dependent on this metabolic reprogramming for their competitive advantage. Importantly, treatment with metformin, an oral anti-diabetic drug with inhibitory activity against complex I in the electron transport chain (ETC), reduced the fitness of Dnmt3aR878H/+ HSCs. Through a multi-omics approach, we discovered that metformin acts by enhancing the methylation potential in Dnmt3aR878H/+ HSPCs and reversing their aberrant DNA CpG methylation and histone H3K27 trimethylation (H3K27me3) profiles. Metformin also reduced the fitness of human DNMT3AR882H HSPCs generated by prime editing. Our findings provide preclinical rationale for investigating metformin as a preventive intervention against illnesses associated with DNMT3AR882 mutation-driven CH in humans.
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Affiliation(s)
| | - Veronique Voisin
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Ali Chegini
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Angelica Varesi
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Alex C.H. Liu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Yitong Yang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Vivian Wang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Abdula Maher
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Eric Grignano
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kira Young
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Yiyan Wu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Martina Fiumara
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Vita-Salute San Raffaele University, Milan, 20132, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Vita-Salute San Raffaele University, Milan, 20132, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
- Vita-Salute San Raffaele University, Milan, 20132, Italy
| | - Federico Gaiti
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shraddha Pai
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Aaron D. Schimmer
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gary D. Bader
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - John E. Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Steven M. Chan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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15
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Guarnera L, Jha BK. TET2 mutation as prototypic clonal hematopoiesis lesion. Semin Hematol 2024; 61:51-60. [PMID: 38431463 PMCID: PMC10978279 DOI: 10.1053/j.seminhematol.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/12/2024] [Accepted: 01/28/2024] [Indexed: 03/05/2024]
Abstract
Loss of function TET2 mutation (TET2MT) is one of the most frequently observed lesions in clonal hematopoiesis (CH). TET2 a member TET-dioxygenase family of enzymes that along with TET1 and TET3, progressively oxidize 5-methyl cytosine (mC) resulting in regulated demethylation of promoter, enhancer and silencer elements of the genome. This process is critical for efficient transcription that determine cell lineage fate, proliferation and survival and the maintenance of the genomic fidelity with aging of the organism. Partial or complete loss-of-function TET2 mutations create regional and contextual DNA hypermethylation leading to gene silencing or activation that result in skewed myeloid differentiation and clonal expansion. In addition to myeloid skewing, loss of TET2 creates differentiation block and provides proliferative advantage to hematopoietic stem and progenitor cells (HSPCs). TET2MT is a prototypical lesion in CH, since the mutant clones dominate during stress hematopoiesis and often associates with evolution of myeloid malignancies. TET2MT clones has unique privilege to create and persist in pro-inflammatory milieu. Despite extensive knowledge regarding biochemical mechanisms underlying distorted myeloid differentiation, and enhanced self-replication of TET2MT HSPC, the mechanistic link of various pathogenesis associated with TET2 loss in CHIP is less understood. Here we review the recent development in TET2 biology and its probable mechanistic link in CH with aging and inflammation. We also explored the therapeutic strategies of targeting TET2MT associated CHIP and the utility of targeting TET2 in normal hematopoiesis and somatic cell reprograming. We explore the biochemical mechanisms and candidate therapies that emerged in last decade of research.
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Affiliation(s)
- Luca Guarnera
- Department of Biomedicine and Prevention, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy; Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Babal K Jha
- Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Center for Immunotherapy and Precision Immuno-Oncology (CITI), Lerner Research Institute (LRI) Cleveland Clinic, Cleveland, OH.
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16
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Tseng YJ, Kageyama Y, Murdaugh RL, Kitano A, Kim JH, Hoegenauer KA, Tiessen J, Smith MH, Uryu H, Takahashi K, Martin JF, Samee MAH, Nakada D. Increased iron uptake by splenic hematopoietic stem cells promotes TET2-dependent erythroid regeneration. Nat Commun 2024; 15:538. [PMID: 38225226 PMCID: PMC10789814 DOI: 10.1038/s41467-024-44718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Hematopoietic stem cells (HSCs) are capable of regenerating the blood system, but the instructive cues that direct HSCs to regenerate particular lineages lost to the injury remain elusive. Here, we show that iron is increasingly taken up by HSCs during anemia and induces erythroid gene expression and regeneration in a Tet2-dependent manner. Lineage tracing of HSCs reveals that HSCs respond to hemolytic anemia by increasing erythroid output. The number of HSCs in the spleen, but not bone marrow, increases upon anemia and these HSCs exhibit enhanced proliferation, erythroid differentiation, iron uptake, and TET2 protein expression. Increased iron in HSCs promotes DNA demethylation and expression of erythroid genes. Suppressing iron uptake or TET2 expression impairs erythroid genes expression and erythroid differentiation of HSCs; iron supplementation, however, augments these processes. These results establish that the physiological level of iron taken up by HSCs has an instructive role in promoting erythroid-biased differentiation of HSCs.
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Affiliation(s)
- Yu-Jung Tseng
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuki Kageyama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rebecca L Murdaugh
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ayumi Kitano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jong Hwan Kim
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin A Hoegenauer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jonathan Tiessen
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mackenzie H Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hidetaka Uryu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - James F Martin
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston, TX, 77030, USA
| | - Md Abul Hassan Samee
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daisuke Nakada
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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17
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Ciriello G, Magnani L, Aitken SJ, Akkari L, Behjati S, Hanahan D, Landau DA, Lopez-Bigas N, Lupiáñez DG, Marine JC, Martin-Villalba A, Natoli G, Obenauf AC, Oricchio E, Scaffidi P, Sottoriva A, Swarbrick A, Tonon G, Vanharanta S, Zuber J. Cancer Evolution: A Multifaceted Affair. Cancer Discov 2024; 14:36-48. [PMID: 38047596 PMCID: PMC10784746 DOI: 10.1158/2159-8290.cd-23-0530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023]
Abstract
Cancer cells adapt and survive through the acquisition and selection of molecular modifications. This process defines cancer evolution. Building on a theoretical framework based on heritable genetic changes has provided insights into the mechanisms supporting cancer evolution. However, cancer hallmarks also emerge via heritable nongenetic mechanisms, including epigenetic and chromatin topological changes, and interactions between tumor cells and the tumor microenvironment. Recent findings on tumor evolutionary mechanisms draw a multifaceted picture where heterogeneous forces interact and influence each other while shaping tumor progression. A comprehensive characterization of the cancer evolutionary toolkit is required to improve personalized medicine and biomarker discovery. SIGNIFICANCE Tumor evolution is fueled by multiple enabling mechanisms. Importantly, genetic instability, epigenetic reprogramming, and interactions with the tumor microenvironment are neither alternative nor independent evolutionary mechanisms. As demonstrated by findings highlighted in this perspective, experimental and theoretical approaches must account for multiple evolutionary mechanisms and their interactions to ultimately understand, predict, and steer tumor evolution.
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Affiliation(s)
- Giovanni Ciriello
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Luca Magnani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Epigenetic Plasticity and Evolution Laboratory, Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sarah J. Aitken
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Leila Akkari
- Division of Tumor Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Douglas Hanahan
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Dan A. Landau
- New York Genome Center, New York, New York
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Darío G. Lupiáñez
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, Leuven, Belgium
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Anna C. Obenauf
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Elisa Oricchio
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Paola Scaffidi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Cancer Epigenetic Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Sottoriva
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Giovanni Tonon
- Vita-Salute San Raffaele University, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sakari Vanharanta
- Translational Cancer Medicine Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
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18
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Zhang Y, Liu F. The evolving views of hematopoiesis: from embryo to adulthood and from in vivo to in vitro. J Genet Genomics 2024; 51:3-15. [PMID: 37734711 DOI: 10.1016/j.jgg.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
The hematopoietic system composed of hematopoietic stem and progenitor cells (HSPCs) and their differentiated lineages serves as an ideal model to uncover generic principles of cell fate transitions. From gastrulation onwards, there successively emerge primitive hematopoiesis (that produces specialized hematopoietic cells), pro-definitive hematopoiesis (that produces lineage-restricted progenitor cells), and definitive hematopoiesis (that produces multipotent HSPCs). These nascent lineages develop in several transient hematopoietic sites and finally colonize into lifelong hematopoietic sites. The development and maintenance of hematopoietic lineages are orchestrated by cell-intrinsic gene regulatory networks and cell-extrinsic microenvironmental cues. Owing to the progressive methodology (e.g., high-throughput lineage tracing and single-cell functional and omics analyses), our understanding of the developmental origin of hematopoietic lineages and functional properties of certain hematopoietic organs has been updated; meanwhile, new paradigms to characterize rare cell types, cell heterogeneity and its causes, and comprehensive regulatory landscapes have been provided. Here, we review the evolving views of HSPC biology during developmental and postnatal hematopoiesis. Moreover, we discuss recent advances in the in vitro induction and expansion of HSPCs, with a focus on the implications for clinical applications.
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Affiliation(s)
- Yifan Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Feng Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China; State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China.
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19
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Isobe T, Kucinski I, Barile M, Wang X, Hannah R, Bastos HP, Chabra S, Vijayabaskar M, Sturgess KH, Williams MJ, Giotopoulos G, Marando L, Li J, Rak J, Gozdecka M, Prins D, Shepherd MS, Watcham S, Green AR, Kent DG, Vassiliou GS, Huntly BJ, Wilson NK, Göttgens B. Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes. CELL GENOMICS 2023; 3:100426. [PMID: 38116120 PMCID: PMC10726426 DOI: 10.1016/j.xgen.2023.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 12/21/2023]
Abstract
Acute myeloid leukemia (AML) and myeloid neoplasms develop through acquisition of somatic mutations that confer mutation-specific fitness advantages to hematopoietic stem and progenitor cells. However, our understanding of mutational effects remains limited to the resolution attainable within immunophenotypically and clinically accessible bulk cell populations. To decipher heterogeneous cellular fitness to preleukemic mutational perturbations, we performed single-cell RNA sequencing of eight different mouse models with driver mutations of myeloid malignancies, generating 269,048 single-cell profiles. Our analysis infers mutation-driven perturbations in cell abundance, cellular lineage fate, cellular metabolism, and gene expression at the continuous resolution, pinpointing cell populations with transcriptional alterations associated with differentiation bias. We further develop an 11-gene scoring system (Stem11) on the basis of preleukemic transcriptional signatures that predicts AML patient outcomes. Our results demonstrate that a single-cell-resolution deep characterization of preleukemic biology has the potential to enhance our understanding of AML heterogeneity and inform more effective risk stratification strategies.
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Affiliation(s)
- Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Melania Barile
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Xiaonan Wang
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Rebecca Hannah
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Hugo P. Bastos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Shirom Chabra
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - M.S. Vijayabaskar
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Katherine H.M. Sturgess
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Matthew J. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Juan Li
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Malgorzata Gozdecka
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Prins
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Mairi S. Shepherd
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Sam Watcham
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Anthony R. Green
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - David G. Kent
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Brian J.P. Huntly
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Nicola K. Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
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20
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Zhang YW, Schönberger K, Cabezas‐Wallscheid N. Bidirectional interplay between metabolism and epigenetics in hematopoietic stem cells and leukemia. EMBO J 2023; 42:e112348. [PMID: 38010205 PMCID: PMC10711668 DOI: 10.15252/embj.2022112348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 11/29/2023] Open
Abstract
During the last decades, remarkable progress has been made in further understanding the complex molecular regulatory networks that maintain hematopoietic stem cell (HSC) function. Cellular and organismal metabolisms have been shown to directly instruct epigenetic alterations, and thereby dictate stem cell fate, in the bone marrow. Epigenetic regulatory enzymes are dependent on the availability of metabolites to facilitate DNA- and histone-modifying reactions. The metabolic and epigenetic features of HSCs and their downstream progenitors can be significantly altered by environmental perturbations, dietary habits, and hematological diseases. Therefore, understanding metabolic and epigenetic mechanisms that regulate healthy HSCs can contribute to the discovery of novel metabolic therapeutic targets that specifically eliminate leukemia stem cells while sparing healthy HSCs. Here, we provide an in-depth review of the metabolic and epigenetic interplay regulating hematopoietic stem cell fate. We discuss the influence of metabolic stress stimuli, as well as alterations occurring during leukemic development. Additionally, we highlight recent therapeutic advancements toward eradicating acute myeloid leukemia cells by intervening in metabolic and epigenetic pathways.
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Affiliation(s)
- Yu Wei Zhang
- Max Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
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21
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McClatchy J, Strogantsev R, Wolfe E, Lin HY, Mohammadhosseini M, Davis BA, Eden C, Goldman D, Fleming WH, Conley P, Wu G, Cimmino L, Mohammed H, Agarwal A. Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells. Nat Commun 2023; 14:8102. [PMID: 38062031 PMCID: PMC10703894 DOI: 10.1038/s41467-023-43697-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined as a single hematopoietic stem/progenitor cell (HSPC) gaining selective advantage over a broader range of HSPCs. When linked to somatic mutations in myeloid malignancy-associated genes, such as TET2-mediated clonal hematopoiesis of indeterminate potential or CHIP, it represents increased risk for hematological malignancies and cardiovascular disease. IL1β is elevated in patients with CHIP, however, its effect is not well understood. Here we show that IL1β promotes expansion of pro-inflammatory monocytes/macrophages, coinciding with a failure in the demethylation of lymphoid and erythroid lineage associated enhancers and transcription factor binding sites, in a mouse model of CHIP with hematopoietic-cell-specific deletion of Tet2. DNA-methylation is significantly lost in wild type HSPCs upon IL1β administration, which is resisted by Tet2-deficient HSPCs, and thus IL1β enhances the self-renewing ability of Tet2-deficient HSPCs by upregulating genes associated with self-renewal and by resisting demethylation of transcription factor binding sites related to terminal differentiation. Using aged mouse models and human progenitors, we demonstrate that targeting IL1 signaling could represent an early intervention strategy in preleukemic disorders. In summary, our results show that Tet2 is an important mediator of an IL1β-promoted epigenetic program to maintain the fine balance between self-renewal and lineage differentiation during hematopoiesis.
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Affiliation(s)
- J McClatchy
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - R Strogantsev
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - E Wolfe
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - H Y Lin
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - M Mohammadhosseini
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - B A Davis
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - C Eden
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - D Goldman
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, OR, USA
| | - W H Fleming
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, OR, USA
| | - P Conley
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - G Wu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - L Cimmino
- University of Miami, Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miami, USA
| | - H Mohammed
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - A Agarwal
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA.
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA.
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
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22
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Ding L, Oh S, Shrestha J, Lam A, Wang Y, Radfar P, Warkiani ME. Scaling up stem cell production: harnessing the potential of microfluidic devices. Biotechnol Adv 2023; 69:108271. [PMID: 37844769 DOI: 10.1016/j.biotechadv.2023.108271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/08/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Stem cells are specialised cells characterised by their unique ability to both self-renew and transform into a wide array of specialised cell types. The widespread interest in stem cells for regenerative medicine and cultivated meat has led to a significant demand for these cells in both research and practical applications. Despite the growing need for stem cell manufacturing, the industry faces significant obstacles, including high costs for equipment and maintenance, complicated operation, and low product quality and yield. Microfluidic technology presents a promising solution to the abovementioned challenges. As an innovative approach for manipulating liquids and cells within microchannels, microfluidics offers a plethora of advantages at an industrial scale. These benefits encompass low setup costs, ease of operation and multiplexing, minimal energy consumption, and the added advantage of being labour-free. This review presents a thorough examination of the prominent microfluidic technologies employed in stem cell research and explores their promising applications in the burgeoning stem cell industry. It thoroughly examines how microfluidics can enhance cell harvesting from tissue samples, facilitate mixing and cryopreservation, streamline microcarrier production, and efficiently conduct cell separation, purification, washing, and final cell formulation post-culture.
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Affiliation(s)
- Lin Ding
- Smart MCs Pty Ltd, Ultimo, Sydney, 2007, Australia.
| | - Steve Oh
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Alan Lam
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Yaqing Wang
- School of Biomedical Engineering, University of Science and Technology of China, Hefei 230026, China; Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Payar Radfar
- Smart MCs Pty Ltd, Ultimo, Sydney, 2007, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia..
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23
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Hong T, Li J, Guo L, Cavalier M, Wang T, Dou Y, DeLaFuente A, Fang S, Guzman A, Wohlan K, Kapadia C, Rosas C, Yang Y, Yin CC, Li S, You MJ, Cheng X, Goodell MA, Zhou Y, Huang Y. TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells. NATURE AGING 2023; 3:1387-1400. [PMID: 37884767 DOI: 10.1038/s43587-023-00505-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
DNA methylation deregulation at partially methylated domains (PMDs) represents an epigenetic signature of aging and cancer, yet the underlying molecular basis and resulting biological consequences remain unresolved. We report herein a mechanistic link between disrupted DNA methylation at PMDs and the spatial relocalization of H3K9me3-marked heterochromatin in aged hematopoietic stem and progenitor cells (HSPCs) or those with impaired DNA methylation. We uncover that TET2 modulates the spatial redistribution of H3K9me3-marked heterochromatin to mediate the upregulation of endogenous retroviruses (ERVs) and interferon-stimulated genes (ISGs), hence contributing to functional decline of aged HSPCs. TET2-deficient HSPCs retain perinuclear distribution of heterochromatin and exhibit age-related clonal expansion. Reverse transcriptase inhibitors suppress ERVs and ISGs expression, thereby restoring age-related defects in aged HSPCs. Collectively, our findings deepen the understanding of the functional interplay between DNA methylation and histone modifications, which is vital for maintaining heterochromatin function and safeguarding genome stability in stem cells.
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Affiliation(s)
- Tingting Hong
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Jia Li
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Lei Guo
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Maryn Cavalier
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Tianlu Wang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yaling Dou
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Aaron DeLaFuente
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Shaohai Fang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Anna Guzman
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Katherina Wohlan
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Chiraag Kapadia
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Carina Rosas
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yaling Yang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Cameron Yin
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoying Li
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M James You
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular Cell Biology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA.
| | - Yun Huang
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Houston, TX, USA.
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24
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Albinati L, Bianchi A, Beekman R. The emerging field of opportunities for single-cell DNA methylation studies in hematology and beyond. Front Mol Biosci 2023; 10:1286716. [PMID: 37954981 PMCID: PMC10637949 DOI: 10.3389/fmolb.2023.1286716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Affiliation(s)
- Leone Albinati
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Agostina Bianchi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Renée Beekman
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre Nacional d’Anàlisi Genòmica (CNAG), Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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25
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Scott TJ, Hansen TJ, McArthur E, Hodges E. Cross-tissue patterns of DNA hypomethylation reveal genetically distinct histories of cell development. BMC Genomics 2023; 24:623. [PMID: 37858046 PMCID: PMC10588161 DOI: 10.1186/s12864-023-09622-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/24/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Establishment of DNA methylation (DNAme) patterns is essential for balanced multi-lineage cellular differentiation, but exactly how these patterns drive cellular phenotypes is unclear. While > 80% of CpG sites are stably methylated, tens of thousands of discrete CpG loci form hypomethylated regions (HMRs). Because they lack DNAme, HMRs are considered transcriptionally permissive, but not all HMRs actively regulate genes. Unlike promoter HMRs, a subset of non-coding HMRs is cell type-specific and enriched for tissue-specific gene regulatory functions. Our data further argues not only that HMR establishment is an important step in enforcing cell identity, but also that cross-cell type and spatial HMR patterns are functionally informative of gene regulation. RESULTS To understand the significance of non-coding HMRs, we systematically dissected HMR patterns across diverse human cell types and developmental timepoints, including embryonic, fetal, and adult tissues. Unsupervised clustering of 126,104 distinct HMRs revealed that levels of HMR specificity reflects a developmental hierarchy supported by enrichment of stage-specific transcription factors and gene ontologies. Using a pseudo-time course of development from embryonic stem cells to adult stem and mature hematopoietic cells, we find that most HMRs observed in differentiated cells (~ 60%) are established at early developmental stages and accumulate as development progresses. HMRs that arise during differentiation frequently (~ 35%) establish near existing HMRs (≤ 6 kb away), leading to the formation of HMR clusters associated with stronger enhancer activity. Using SNP-based partitioned heritability from GWAS summary statistics across diverse traits and clinical lab values, we discovered that genetic contribution to trait heritability is enriched within HMRs. Moreover, the contribution of heritability to cell-relevant traits increases with both increasing HMR specificity and HMR clustering, supporting the role of distinct HMR subsets in regulating normal cell function. CONCLUSIONS Our results demonstrate that the entire HMR repertoire within a cell-type, rather than just the cell type-specific HMRs, stores information that is key to understanding and predicting cellular phenotypes. Ultimately, these data provide novel insights into how DNA hypo-methylation provides genetically distinct historical records of a cell's journey through development, highlighting HMRs as functionally distinct from other epigenomic annotations.
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Affiliation(s)
- Timothy J Scott
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Tyler J Hansen
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Evonne McArthur
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Emily Hodges
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
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26
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Yang J, Liu Y, Yin H, Xie S, Zhang L, Dong X, Ni H, Bu W, Ma H, Liu P, Zhu H, Guo R, Sun L, Wu Y, Qin J, Sun B, Li D, Luo HR, Liu M, Xuan C, Zhou J. HDAC6 deacetylates IDH1 to promote the homeostasis of hematopoietic stem and progenitor cells. EMBO Rep 2023; 24:e56009. [PMID: 37642636 PMCID: PMC10561360 DOI: 10.15252/embr.202256009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are cells mainly present in the bone marrow and capable of forming mature blood cells. However, the epigenetic mechanisms governing the homeostasis of HSPCs remain elusive. Here, we demonstrate an important role for histone deacetylase 6 (HDAC6) in regulating this process. Our data show that the percentage of HSPCs in Hdac6 knockout mice is lower than in wild-type mice due to decreased HSPC proliferation. HDAC6 interacts with isocitrate dehydrogenase 1 (IDH1) and deacetylates IDH1 at lysine 233. The deacetylation of IDH1 inhibits its catalytic activity and thereby decreases the 5-hydroxymethylcytosine level of ten-eleven translocation 2 (TET2) target genes, changing gene expression patterns to promote the proliferation of HSPCs. These findings uncover a role for HDAC6 and IDH1 in regulating the homeostasis of HSPCs and may have implications for the treatment of hematological diseases.
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Affiliation(s)
- Jia Yang
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Hanxiao Yin
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Songbo Xie
- Center for Cell Structure and Function, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of ShandongShandong Normal UniversityJinanChina
| | - Linlin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Xifeng Dong
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Hua Ni
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Weiwen Bu
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Hongbo Ma
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Peng Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Haiyan Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Rongxia Guo
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Lei Sun
- Center for Cell Structure and Function, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of ShandongShandong Normal UniversityJinanChina
| | - Yue Wu
- Center for Cell Structure and Function, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of ShandongShandong Normal UniversityJinanChina
| | - Juan Qin
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Baofa Sun
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Dengwen Li
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
| | - Hongbo R Luo
- Department of Pathology, Department of Laboratory Medicine, Harvard Medical SchoolChildren's Hospital Boston, Dana‐Farber/Harvard Cancer CenterBostonMAUSA
| | - Min Liu
- Laboratory of Tissue HomeostasisHaihe Laboratory of Cell EcosystemTianjinChina
| | - Chenghao Xuan
- The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Jun Zhou
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, Tianjin Key Laboratory of Protein Science, College of Life SciencesNankai UniversityTianjinChina
- Center for Cell Structure and Function, College of Life Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of ShandongShandong Normal UniversityJinanChina
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27
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Huang Y, Li L, An G, Yang X, Cui M, Song X, Lin J, Zhang X, Yao Z, Wan C, Zhou C, Zhao J, Song K, Ren S, Xia X, Fu X, Lan Y, Hu X, Wang W, Wang M, Zheng Y, Miao K, Bai X, Hutchins AP, Chang G, Gao S, Zhao XY. Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination. Nat Cell Biol 2023; 25:1520-1534. [PMID: 37723297 DOI: 10.1038/s41556-023-01232-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
Abstract
Human spermatogenesis is a highly ordered process; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes using the modified single-cell chromatin overall omic-scale landscape sequencing approach, we revealed that the transcriptional changes throughout human spermatogenesis were correlated with chromatin accessibility changes. In particular, we identified a set of transcription factors and cis elements with potential functions. A round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. Aberrant DNA hypermethylation could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination and fertility. Our work provides multi-omics landscapes of human spermatogenesis at single-cell resolution and offers insights into the association between DNA demethylation and male meiotic recombination.
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Affiliation(s)
- Yaping Huang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Geng An
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xinyan Yang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Manman Cui
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiuling Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jing Lin
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xiaoling Zhang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Zhaokai Yao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Cong Wan
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Cai Zhou
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Jiexiang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Ke Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Shaofang Ren
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xinyu Xia
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Xin Fu
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Yu Lan
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xuesong Hu
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Wen Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Mei Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Yi Zheng
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Kai Miao
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, P. R. China
| | - Xiaochun Bai
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, P. R. China
| | - Gang Chang
- Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, P. R. China.
| | - Shuai Gao
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China.
| | - Xiao-Yang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, P. R. China.
- Guangdong Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, P. R. China.
- Key Laboratory of Mental Health of the Ministry of Education, Guangzhou, P. R. China.
- Department of Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, P. R. China.
- National Clinical Research Center for Kidney Disease, Guangzhou, P. R. China.
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28
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Carty SA. Biological insights into the role of TET2 in T cell lymphomas. Front Oncol 2023; 13:1199108. [PMID: 37841428 PMCID: PMC10570544 DOI: 10.3389/fonc.2023.1199108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
Peripheral T cell lymphomas (PTCL) are a heterogenous group of mature T cell lymphomas with an overall poor prognosis. Understanding the molecular heterogeneity in PTCL subtypes may lead to improved understanding of the underlying biological mechanisms driving these diseases. Mutations in the epigenetic regulator TET2 are among the most frequent mutations identified in PTCL, with the highest frequency in angioimmunoblastic T cell lymphomas and other nodal T follicular helper (TFH) lymphomas. This review dissects the role of TET2 in nodal TFH cell lymphomas with a focus on emerging biological insights into the molecular mechanism promoting lymphomagenesis and the potential for epigenetic therapies to improve clinical outcomes.
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Affiliation(s)
- Shannon A. Carty
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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29
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Cheng G, Wu J, Ji M, Hu W, Wu C, Jiang J. TET2 inhibits the proliferation and metastasis of lung adenocarcinoma cells via activation of the cGAS-STING signalling pathway. BMC Cancer 2023; 23:825. [PMID: 37667220 PMCID: PMC10478367 DOI: 10.1186/s12885-023-11343-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Effective identification and development of new molecular methods for the diagnosis, treatment and prognosis of lung adenocarcinoma (LUAD) remains an urgent clinical need. DNA methylation patterns at cytosine bases in the genome are closely related to gene expression, and abnormal DNA methylation is frequently observed in various cancers. The ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine (5mC) and promote locus-specific DNA methylation reversal. This study aimed to explore the role of the TET2 protein and its downstream effector, 5-hmC/5-mC DNA modification, in LUAD progression. METHODS The expression of TET2 was analysed by real-time PCR, Western blotting and immunohistochemistry. The 5-hmC DNA content was determined by a colorimetric kit. Activation of the cGAS-STING signalling pathway was evaluated by Western blotting. CCK-8, wound healing and Transwell assays were performed to evaluate the effect of TET2 on cell proliferation, migration and invasion abilities. A xenograft model was used to analyse the effect of TET2 on the tumorigenic ability of A549 cells. RESULTS TET2 overexpression decreased proliferation and metastasis of A549 and H1975 cells in vitro and in vivo. However, TET2 knockdown dramatically enhanced the proliferation, migration and invasion of A549 and H1975 cells. Mechanistically, activation of the cGAS-STING signalling pathway is critical for the TET2-mediated suppression of LUAD cell tumorigenesis and metastasis. CONCLUSION In this study, we demonstrate a tumour suppressor role of TET2 in LUAD, providing new potential molecular therapeutic targets and clinical therapies for patients with non-small cell lung cancer.
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Affiliation(s)
- Gui Cheng
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China
| | - Jun Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China
| | - Mei Ji
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China
| | - Wenwei Hu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China
| | - Changping Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China.
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital, Soochow University, 185 Juqian Street, Changzhou, 213003, P.R. China.
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30
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Lara-Astiaso D, Goñi-Salaverri A, Mendieta-Esteban J, Narayan N, Del Valle C, Gross T, Giotopoulos G, Beinortas T, Navarro-Alonso M, Aguado-Alvaro LP, Zazpe J, Marchese F, Torrea N, Calvo IA, Lopez CK, Alignani D, Lopez A, Saez B, Taylor-King JP, Prosper F, Fortelny N, Huntly BJP. In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis. Nat Genet 2023; 55:1542-1554. [PMID: 37580596 PMCID: PMC10484791 DOI: 10.1038/s41588-023-01471-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/11/2023] [Indexed: 08/16/2023]
Abstract
Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.
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Affiliation(s)
- David Lara-Astiaso
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
| | | | | | - Nisha Narayan
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Cynthia Del Valle
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - George Giotopoulos
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Tumas Beinortas
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Mar Navarro-Alonso
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Jon Zazpe
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Francesco Marchese
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Natalia Torrea
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Isabel A Calvo
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Cecile K Lopez
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Diego Alignani
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Aitziber Lopez
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Borja Saez
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Felipe Prosper
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Nikolaus Fortelny
- Department of Biosciences & Medical Biology, University of Salzburg, Salzburg, Austria.
| | - Brian J P Huntly
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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31
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Sobieralski P, Wasąg B, Leszczyńska A, Żuk M, Bieniaszewska M. The molecular profile in patients with polycythemia vera and essential thrombocythemia is dynamic and correlates with disease's phenotype. Front Oncol 2023; 13:1224590. [PMID: 37671053 PMCID: PMC10475996 DOI: 10.3389/fonc.2023.1224590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction Polycythemia vera (PV) and essential thrombocythemia (ET) are diseases driven by canonical mutations in JAK2, CALR, or MPL gene. Previous studies revealed that in addition to driver mutations, patients with PV and ET can harbor other mutations in various genes, with no established impact on disease phenotype. We hypothesized that the molecular profile of patients with PV and ET is dynamic throughout the disease. Methods In this study, we performed a 37-gene targeted next-generation sequencing panel on the DNA samples collected from 49 study participants in two-time points, separated by 78-141 months. We identified 78 variants across 37 analyzed genes in the study population. Results By analyzing the change in variant allele frequencies and revealing the acquisition of new mutations during the disease, we confirmed the dynamic nature of the molecular profile of patients with PV and ET. We found connections between specific variants with the development of secondary myelofibrosis, thrombotic events, and response to treatment. We confronted our results with existing conventional and mutation-enhanced prognostic systems, showing the limited utility of available prognostic tools. Discussion The results of this study underline the significance of repeated molecular testing in patients with PV and ET and indicate the need for further research within this field to better understand the disease and improve available prognostic tools.
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Affiliation(s)
- Patryk Sobieralski
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasąg
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Aleksandra Leszczyńska
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Monika Żuk
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Maria Bieniaszewska
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
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32
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Gutierrez-Rodrigues F, Kusne Y, Fernandez J, Lasho T, Shalhoub R, Ma X, Alessi H, Finke C, Koster MJ, Mangaonkar A, Warrington KJ, Begna K, Xie Z, Ombrello AK, Viswanatha D, Ferrada M, Wilson L, Go R, Kourelis T, Reichard K, Olteanu H, Darden I, Hironaka D, Alemu L, Kajigaya S, Rosenzweig S, Calado RT, Groarke EM, Kastner DL, Calvo KR, Wu CO, Grayson PC, Young NS, Beck DB, Patel BA, Patnaik MM. Spectrum of clonal hematopoiesis in VEXAS syndrome. Blood 2023; 142:244-259. [PMID: 37084382 PMCID: PMC10375269 DOI: 10.1182/blood.2022018774] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/23/2023] Open
Abstract
Vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome is caused by somatic mutations in UBA1 (UBA1mut) and characterized by heterogenous systemic autoinflammation and progressive hematologic manifestations, meeting criteria for myelodysplastic syndrome (MDS) and plasma cell dyscrasias. The landscape of myeloid-related gene mutations leading to typical clonal hematopoiesis (CH) in these patients is unknown. Retrospectively, we screened 80 patients with VEXAS for CH in their peripheral blood (PB) and correlated the findings with clinical outcomes in 77 of them. UBA1mut were most common at hot spot p.M41 (median variant allele frequency [VAF] = 75%). Typical CH mutations cooccurred with UBA1mut in 60% of patients, mostly in DNMT3A and TET2, and were not associated with inflammatory or hematologic manifestations. In prospective single-cell proteogenomic sequencing (scDNA), UBA1mut was the dominant clone, present mostly in branched clonal trajectories. Based on integrated bulk and scDNA analyses, clonality in VEXAS followed 2 major patterns: with either typical CH preceding UBA1mut selection in a clone (pattern 1) or occurring as an UBA1mut subclone or in independent clones (pattern 2). VAF in the PB differed markedly between DNMT3A and TET2 clones (median VAF of 25% vs 1%). DNMT3A and TET2 clones associated with hierarchies representing patterns 1 and 2, respectively. Overall survival for all patients was 60% at 10 years. Transfusion-dependent anemia, moderate thrombocytopenia, and typical CH mutations, each correlated with poor outcome. In VEXAS, UBA1mut cells are the primary cause of systemic inflammation and marrow failure, being a new molecularly defined somatic entity associated with MDS. VEXAS-associated MDS is distinct from classical MDS in its presentation and clinical course.
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Affiliation(s)
| | - Yael Kusne
- Division of Hematology and Oncology, Mayo Clinic, Phoenix, AZ
| | - Jenna Fernandez
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Terra Lasho
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Xiaoyang Ma
- Hematology Branch, National Heart, Lung, and Blood Institute, National institutes of Health, Bethesda, MD
| | - Hugh Alessi
- Vasculitis Translational Research Program, National Institute of Arthritis and Musculoskeletal, and Skin Diseases, National institutes of Health, Bethesda, MD
| | - Christy Finke
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Matthew J. Koster
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Abhishek Mangaonkar
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Kenneth J. Warrington
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Kebede Begna
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Zhuoer Xie
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
| | - Amanda K. Ombrello
- Inflammatory Disease Section, National Human Genome Research Institute, National institute of Health, Bethesda, MD
| | - David Viswanatha
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Marcela Ferrada
- Vasculitis Translational Research Program, National Institute of Arthritis and Musculoskeletal, and Skin Diseases, National institutes of Health, Bethesda, MD
| | - Lorena Wilson
- Inflammatory Disease Section, National Human Genome Research Institute, National institute of Health, Bethesda, MD
| | - Ronald Go
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Kaaren Reichard
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Horatiu Olteanu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Ivana Darden
- Hematology Branch, National Heart, Lung, and Blood Institute, National institutes of Health, Bethesda, MD
| | - Dalton Hironaka
- Hematology Branch, National Heart, Lung, and Blood Institute, National institutes of Health, Bethesda, MD
| | - Lemlem Alemu
- Hematology Branch, National Heart, Lung, and Blood Institute, National institutes of Health, Bethesda, MD
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National institutes of Health, Bethesda, MD
| | - Sofia Rosenzweig
- Inflammatory Disease Section, National Human Genome Research Institute, National institute of Health, Bethesda, MD
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Emma M. Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National institutes of Health, Bethesda, MD
| | - Daniel L. Kastner
- Inflammatory Disease Section, National Human Genome Research Institute, National institute of Health, Bethesda, MD
| | - Katherine R. Calvo
- Hematology Section, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Colin O. Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Peter C. Grayson
- Vasculitis Translational Research Program, National Institute of Arthritis and Musculoskeletal, and Skin Diseases, National institutes of Health, Bethesda, MD
| | - Neal S. Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National institutes of Health, Bethesda, MD
| | - David B. Beck
- Inflammatory Disease Section, National Human Genome Research Institute, National institute of Health, Bethesda, MD
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY
| | - Bhavisha A. Patel
- Hematology Branch, National Heart, Lung, and Blood Institute, National institutes of Health, Bethesda, MD
| | - Mrinal M. Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN
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Yokomizo-Nakano T, Hamashima A, Kubota S, Bai J, Sorin S, Sun Y, Kikuchi K, Iimori M, Morii M, Kanai A, Iwama A, Huang G, Kurotaki D, Takizawa H, Matsui H, Sashida G. Exposure to microbial products followed by loss of Tet2 promotes myelodysplastic syndrome via remodeling HSCs. J Exp Med 2023; 220:e20220962. [PMID: 37071125 PMCID: PMC10120406 DOI: 10.1084/jem.20220962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/11/2023] [Accepted: 03/28/2023] [Indexed: 04/19/2023] Open
Abstract
Aberrant innate immune signaling in myelodysplastic syndrome (MDS) hematopoietic stem/progenitor cells (HSPCs) has been implicated as a driver of the development of MDS. We herein demonstrated that a prior stimulation with bacterial and viral products followed by loss of the Tet2 gene facilitated the development of MDS via up-regulating the target genes of the Elf1 transcription factor and remodeling the epigenome in hematopoietic stem cells (HSCs) in a manner that was dependent on Polo-like kinases (Plk) downstream of Tlr3/4-Trif signaling but did not increase genomic mutations. The pharmacological inhibition of Plk function or the knockdown of Elf1 expression was sufficient to prevent the epigenetic remodeling in HSCs and diminish the enhanced clonogenicity and the impaired erythropoiesis. Moreover, this Elf1-target signature was significantly enriched in MDS HSPCs in humans. Therefore, prior infection stress and the acquisition of a driver mutation remodeled the transcriptional and epigenetic landscapes and cellular functions in HSCs via the Trif-Plk-Elf1 axis, which promoted the development of MDS.
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Affiliation(s)
- Takako Yokomizo-Nakano
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ai Hamashima
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Sho Kubota
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jie Bai
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Supannika Sorin
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Yuqi Sun
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenta Kikuchi
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mihoko Iimori
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mariko Morii
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Gang Huang
- Department of Cell Systems & Anatomy, Department of Pathology and Laboratory Medicine, UT Health San Antonio, Joe R. and Teresa Lozano Long School of Medicine, Mays Cancer Center at UT Health San Antonio, San Antonio, TX, USA
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hitoshi Takizawa
- Laboratory of Stem Cell Stress, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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34
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Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Salazar MA, Hentges LD, Mickute G, Clark K, Sopp P, Davies JOJ, Hughes JR, Vyas P. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell 2023; 30:722-740.e11. [PMID: 37146586 DOI: 10.1016/j.stem.2023.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.
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Affiliation(s)
- Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angus Groom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Simone G Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - E Ravza Gür
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Batchimeg Usukhbayar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Mirian Angulo Salazar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lance D Hentges
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gerda Mickute
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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35
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Methylation-sensitive transcription-enhanced single-molecule biosensing of DNA methylation in cancer cells and tissues. Anal Chim Acta 2023; 1251:340996. [PMID: 36925287 DOI: 10.1016/j.aca.2023.340996] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
As a major epigenetic modification, DNA methylation participates in diverse cellular functions and emerges as a promising biomarker for disease diagnosis and monitoring. Herein, we developed a methylation-sensitive transcription-enhanced single-molecule biosensor to detect DNA methylation in human cells and tissues. In this biosensor, a rationally designed transcription machine is split into two parts including a promoter sequence (probe-P) for initiating transcription and a template sequence (probe-T) for RNA synthesis. The presence of specific DNA methylation leads to the formation of full-length transcription machine through sequence-specific ligation of probe-P and probe-T, initiating the synthesis of abundant ssRNA transcripts. The resultant ssRNAs can activate CRISPR/Cas12a to catalyze cyclic cleavage of fluorophore- and quencher-dual labeled signal probes, resulting in the recovery of the fluorophore signal that can be quantified by single-molecule detection. Taking advantages of the high-fidelity ligation of split transcription machine and the high efficiency of transcription- and CRISPR/Cas12a cleavage-mediated dual signal amplification, this single-molecule biosensor achieves a low detection limit of 337 aM and high selectivity. Moreover, it can distinguish 0.01% methylation level, and even accurately detect genomic DNA methylation in single cell and clinical samples, providing a powerful tool for epigenetic researches and clinical diagnostics.
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36
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Beneyto-Calabuig S, Merbach AK, Kniffka JA, Antes M, Szu-Tu C, Rohde C, Waclawiczek A, Stelmach P, Gräßle S, Pervan P, Janssen M, Landry JJM, Benes V, Jauch A, Brough M, Bauer M, Besenbeck B, Felden J, Bäumer S, Hundemer M, Sauer T, Pabst C, Wickenhauser C, Angenendt L, Schliemann C, Trumpp A, Haas S, Scherer M, Raffel S, Müller-Tidow C, Velten L. Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia. Cell Stem Cell 2023; 30:706-721.e8. [PMID: 37098346 DOI: 10.1016/j.stem.2023.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/05/2023] [Accepted: 03/30/2023] [Indexed: 04/27/2023]
Abstract
Inter-patient variability and the similarity of healthy and leukemic stem cells (LSCs) have impeded the characterization of LSCs in acute myeloid leukemia (AML) and their differentiation landscape. Here, we introduce CloneTracer, a novel method that adds clonal resolution to single-cell RNA-seq datasets. Applied to samples from 19 AML patients, CloneTracer revealed routes of leukemic differentiation. Although residual healthy and preleukemic cells dominated the dormant stem cell compartment, active LSCs resembled their healthy counterpart and retained erythroid capacity. By contrast, downstream myeloid progenitors constituted a highly aberrant, disease-defining compartment: their gene expression and differentiation state affected both the chemotherapy response and leukemia's ability to differentiate into transcriptomically normal monocytes. Finally, we demonstrated the potential of CloneTracer to identify surface markers misregulated specifically in leukemic cells. Taken together, CloneTracer reveals a differentiation landscape that mimics its healthy counterpart and may determine biology and therapy response in AML.
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Affiliation(s)
- Sergi Beneyto-Calabuig
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anne Kathrin Merbach
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany
| | - Jonas-Alexander Kniffka
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Magdalena Antes
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Chelsea Szu-Tu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Christian Rohde
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany
| | - Alexander Waclawiczek
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Patrick Stelmach
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Sarah Gräßle
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Philip Pervan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Maike Janssen
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, 69120 Heidelberg, Germany
| | - Michaela Brough
- Institute of Human Genetics, University of Heidelberg, 69120 Heidelberg, Germany
| | - Marcus Bauer
- Institute of Pathology, University Hospital Halle (Saale), Martin-Luther-University Halle-Wittenberg, 06112 Halle, Germany
| | - Birgit Besenbeck
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Julia Felden
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Sebastian Bäumer
- Department of Medicine A, Hematology and Oncology, University Hospital, Muenster, Germany
| | - Michael Hundemer
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Tim Sauer
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Caroline Pabst
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, University Hospital Halle (Saale), Martin-Luther-University Halle-Wittenberg, 06112 Halle, Germany
| | - Linus Angenendt
- Department of Medicine A, Hematology and Oncology, University Hospital, Muenster, Germany; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christoph Schliemann
- Department of Medicine A, Hematology and Oncology, University Hospital, Muenster, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Michael Scherer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Simon Raffel
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, European Molecular Biology Laboratory (EMBL), University of Heidelberg, 69117 Heidelberg, Germany.
| | - Lars Velten
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Xiao J, Xie J, Zhou B, Liu Y, Lu J, Jiang A, Yao H, Qiu Q, Ding Z, Xue S, Tang X, Qiu H, Chen S, Shen H, Wu D, Xu Y. RUNX1 together with DAT mutations predicted poor outcome in acute myeloid leukemia. Leuk Lymphoma 2023:1-11. [PMID: 36964663 DOI: 10.1080/10428194.2023.2190433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
We retrospectively explored the prognostic impact of DAT mutations at diagnosis in 122 RUNX1mut AML patients. RUNX1 missense mutation was dominant in the RUNT domain, and frameshift mutation was dominant in the TAD domain. DAT mutations occurred in 38.5% of RUNX1mut AML. After propensity score matching, DATpos patients had worse two-year relapse-free survival (RFS) than DATneg patients (p = .041). Moreover, RUNX1high (VAF ≥ 37.6%) patients showed poorer two-year overall survival (OS) and RFS than RUNX1low (VAF < 37.6%) patients (OS, p = .033; RFS, p = .027), especially in the RUNX1highDATpos group. Additionally, multivariate analysis confirmed that DAT mutations at diagnosis were an independent adverse factor for RFS. There were no significant differences in two-year OS and RFS between DATpos and DATneg patients or between RUNX1high and RUNX1low patients who undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). Collectively, DAT mutations at diagnosis were adverse factors for RFS, and allo-HSCT could likely improve the poor outcomes of these patients.
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Affiliation(s)
- Jinyan Xiao
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Jundan Xie
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Biqi Zhou
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Yujie Liu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Jing Lu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Airui Jiang
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Hong Yao
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Qiaocheng Qiu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Zixuan Ding
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Shengli Xue
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Xiaowen Tang
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Huiying Qiu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Suning Chen
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Hongjie Shen
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Depei Wu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
| | - Yang Xu
- Jiangsu Institute of Haematology, National Clinical Research Center for Haematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Haematology, Soochow University, Suzhou, China
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Shevyrev D, Tereshchenko V, Berezina TN, Rybtsov S. Hematopoietic Stem Cells and the Immune System in Development and Aging. Int J Mol Sci 2023; 24:ijms24065862. [PMID: 36982935 PMCID: PMC10056303 DOI: 10.3390/ijms24065862] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Hematopoietic stem cells (HSCs) support haematopoiesis throughout life and give rise to the whole variety of cells of the immune system. Developing in the early embryo, passing through the precursor stage, and maturing into the first HSCs, they undergo a fairly large number of divisions while maintaining a high regenerative potential due to high repair activity. This potential is greatly reduced in adult HSCs. They go into a state of dormancy and anaerobic metabolism to maintain their stemness throughout life. However, with age, changes occur in the pool of HSCs that negatively affect haematopoiesis and the effectiveness of immunity. Niche aging and accumulation of mutations with age reduces the ability of HSCs to self-renew and changes their differentiation potential. This is accompanied by a decrease in clonal diversity and a disturbance of lymphopoiesis (decrease in the formation of naive T- and B-cells) and the predominance of myeloid haematopoiesis. Aging also affects mature cells, regardless of HSC, therefore, phagocytic activity and the intensity of the oxidative burst decrease, and the efficiency of processing and presentation of antigens by myeloid cells is impaired. Aging cells of innate and adaptive immunity produce factors that form a chronic inflammatory background. All these processes have a serious negative impact on the protective properties of the immune system, increasing inflammation, the risk of developing autoimmune, oncological, and cardiovascular diseases with age. Understanding the mechanisms of reducing the regenerative potential in a comparative analysis of embryonic and aging HSCs, the features of inflammatory aging will allow us to get closer to deciphering the programs for the development, aging, regeneration and rejuvenation of HSCs and the immune system.
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Affiliation(s)
- Daniil Shevyrev
- Centre for Cell Technology and Immunology, Sirius University of Science and Technology, Sirius, 354340 Sochi, Russia
| | - Valeriy Tereshchenko
- Centre for Cell Technology and Immunology, Sirius University of Science and Technology, Sirius, 354340 Sochi, Russia
| | - Tatiana N Berezina
- Department of Scientific Basis of Extreme Psychology, Moscow State University of Psychology and Education, 127051 Moscow, Russia
| | - Stanislav Rybtsov
- Centre for Cell Technology and Immunology, Sirius University of Science and Technology, Sirius, 354340 Sochi, Russia
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH8 9YL, UK
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Fu MP, Merrill SM, Sharma M, Gibson WT, Turvey SE, Kobor MS. Rare diseases of epigenetic origin: Challenges and opportunities. Front Genet 2023; 14:1113086. [PMID: 36814905 PMCID: PMC9939656 DOI: 10.3389/fgene.2023.1113086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.
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Affiliation(s)
- Maggie P. Fu
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mehul Sharma
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - William T. Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Stuart E. Turvey
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor,
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Diplas BH, Ptashkin R, Chou JF, Sabwa S, Foote MB, Rousseau B, Argilés G, White JR, Stewart CM, Bolton K, Chalasani SB, Desai AM, Goldberg Z, Gu P, Li J, Shcherba M, Zervoudakis A, Cercek A, Yaeger R, Segal NH, Ilson DH, Ku GY, Zehir A, Capanu M, Janjigian YY, Diaz LA, Maron SB. Clinical Importance of Clonal Hematopoiesis in Metastatic Gastrointestinal Tract Cancers. JAMA Netw Open 2023; 6:e2254221. [PMID: 36729457 PMCID: PMC9896303 DOI: 10.1001/jamanetworkopen.2022.54221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/12/2022] [Indexed: 02/03/2023] Open
Abstract
Importance Clonal hematopoiesis (CH) has been associated with development of atherosclerosis and leukemia and worse survival among patients with cancer; however, the association with cancer therapy efficacy, in particular immune checkpoint blockade (ICB), and toxicity has not yet been established. Given the widespread use of ICB and the critical role hematopoietic stem cell-derived lymphocytes play in mediating antitumor responses, CH may be associated with therapeutic efficacy and hematologic toxicity. Objective To determine the association between CH and outcomes, hematologic toxicity, and therapeutic efficacy in patients with metastatic gastrointestinal tract cancers being treated with systemic therapy, both in the first-line metastatic treatment setting and in ICB. Design, Setting, and Participants This retrospective cohort study included 633 patients with stage IV colorectal (CRC) and esophagogastric (EGC) cancer who were treated with first-line chemotherapy and/or ICB at Memorial Sloan Kettering Cancer Center. Patients underwent matched tumor and peripheral blood DNA sequencing using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets next-generation sequencing assay between January 1, 2006, and December 31, 2020. Exposures Clonal hematopoiesis-related genetic alterations were identified by next-generation sequencing of patients' tumor and normal blood buffy coat samples, with a subset of these CH alterations annotated as likely putative drivers (CH-PD) based upon previously established criteria. Main Outcomes and Measures Patients with CH and CH-PD in peripheral blood samples were identified, and these findings were correlated with survival outcomes (progression-free survival [PFS] and overall survival [OS]) during first-line chemotherapy and ICB, as well as baseline white blood cell levels and the need for granulocyte colony-stimulating factor (G-CSF) support. Results Among the 633 patients included in the study (390 men [61.6%]; median age, 58 [IQR, 48-66] years), the median age was 52 (IQR, 45-63) years in the CRC group and 61 (IQR, 53-69) years in the EGC group. In the CRC group, 161 of 301 patients (53.5%) were men, compared with 229 of 332 patients (69.0%) in the EGC group. Overall, 62 patients (9.8%) were Asian, 45 (7.1%) were Black or African American, 482 (76.1%) were White, and 44 (7.0%) were of unknown race or ethnicity. Presence of CH was identified in 115 patients with EGC (34.6%) and 83 with CRC (27.6%), with approximately half of these patients harboring CH-PD (CRC group, 44 of 83 [53.0%]; EGC group, 55 of 115 [47.8%]). Patients with EGC and CH-PD exhibited a significantly worse median OS of 16.0 (95% CI, 11.6-22.3) months compared with 21.6 (95% CI, 19.6-24.3) months for those without CH-PD (P = .01). For patients with CRC and EGC, CH and CH-PD were not associated with PFS differences in patients undergoing ICB or first-line chemotherapy. Neither CH nor CH-PD were correlated with baseline leukocyte levels or increased need for G-CSF support. Conclusions and Relevance These findings suggest CH and CH-PD are not directly associated with the treatment course of patients with metastatic gastrointestinal tract cancer receiving cancer-directed therapy.
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Affiliation(s)
- Bill H. Diplas
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F. Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shalom Sabwa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael B. Foote
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benoit Rousseau
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Guillem Argilés
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Caitlin M. Stewart
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York
- New York Genome Center, New York, New York
| | - Kelly Bolton
- Department of Medicine, Washington University Medical School, St Louis, Missouri
| | - Sree B. Chalasani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Avni M. Desai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zoe Goldberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ping Gu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jia Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marina Shcherba
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alice Zervoudakis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neil H. Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David H. Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y. Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y. Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Luis A. Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Steven B. Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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41
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Braun TP, Estabrook J, Schonrock Z, Curtiss BM, Darmusey L, Macaraeg J, Enright T, Coblentz C, Callahan R, Yashar W, Taherinasab A, Mohammed H, Coleman DJ, Druker BJ, Demir E, Lusardi TA, Maxson JE. Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors. Leukemia 2023; 37:478-487. [PMID: 36526735 PMCID: PMC9899319 DOI: 10.1038/s41375-022-01792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
Mutations in the gene Additional Sex-Combs Like 1 (ASXL1) are recurrent in myeloid malignancies as well as the pre-malignant condition clonal hematopoiesis, where they are universally associated with poor prognosis. However, the role of ASXL1 in myeloid lineage maturation is incompletely described. To define the role of ASXL1 in myelopoiesis, we employed single cell RNA sequencing and a murine model of hematopoietic-specific Asxl1 deletion. In granulocyte progenitors, Asxl1 deletion leads to hyperactivation of MYC and a quantitative decrease in neutrophil production. This loss of granulocyte production was not accompanied by significant changes in the landscape of covalent histone modifications. However, Asxl1 deletion results in a decrease in RNAPII promoter-proximal pausing in granulocyte progenitors, indicative of a global increase in productive transcription. These results suggest that ASXL1 inhibits productive transcription in granulocyte progenitors, identifying a new role for this epigenetic regulator in myeloid development.
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Affiliation(s)
- Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Division of Hematology & Medical Oncology, Oregon
Health & Science University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
| | - Joseph Estabrook
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Zachary Schonrock
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Brittany M. Curtiss
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Lucie Darmusey
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Jommel Macaraeg
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Trevor Enright
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Cody Coblentz
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Rowan Callahan
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - William Yashar
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Akram Taherinasab
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Hisham Mohammed
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Daniel J. Coleman
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Division of Hematology & Medical Oncology, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Theresa A. Lusardi
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
| | - Julia E. Maxson
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
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Morishita S, Hashimoto Y, Furuya C, Edahiro Y, Ochiai T, Shirane S, Inano T, Yasuda H, Ando M, Araki M, Komatsu N. Non-driver gene mutation analysis in a large cohort of polycythemia vera and essential thrombocythemia. Eur J Haematol Suppl 2023; 110:131-136. [PMID: 36208190 DOI: 10.1111/ejh.13882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 01/19/2023]
Abstract
OBJECTIVES A proportion of patients with polycythemia vera (PV) and essential thrombocythemia (ET) harbor non-driver mutations associated with poor prognosis. In this study, we analyzed the frequency of non-driver mutations in a large Japanese PV and ET cohort. Furthermore, we studied the relationship of these mutations and prognosis in Japanese patients. METHODS We enrolled 843 Japanese patients with PV or ET. Non-driver mutations were analyzed by target resequencing using next-generation sequencing. The association of the mutations with the prognosis was estimated using multivariable logistic regression analysis and log-rank test. RESULTS Non-driver mutations were detected in 31.1% and 24.5% patients with PV and ET, respectively. Among them, ASXL1 mutations were identified as a risk factor for leukemic/myelofibrotic transformation in PV and ET patients (hazard ratio: 4.68, p = .006). The higher-risk groups of the mutation-enhanced international prognostic system (MIPSS)-PV and MIPSS-ET incorporating non-driver mutations exhibited significantly shorter overall survival compared with the low-risk group (p < .001). CONCLUSIONS These results implicate the importance of studying non-driver mutations for predicting the prognosis and survival of Japanese PV and ET patients.
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Affiliation(s)
- Soji Morishita
- Laboratory for the Development of Therapies Against MPN, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Advanced Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoshinori Hashimoto
- Advanced Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Department of Hematology, Tottori Prefectural Central Hospital, Tottori, Japan
| | - Chiho Furuya
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoko Edahiro
- Advanced Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomonori Ochiai
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shuichi Shirane
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tadaaki Inano
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hajime Yasuda
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miki Ando
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Marito Araki
- Laboratory for the Development of Therapies Against MPN, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Advanced Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Norio Komatsu
- Laboratory for the Development of Therapies Against MPN, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Advanced Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan.,PharmaEssentia Japan K.K., Tokyo, Japan
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43
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Fortin J, Chiang MF, Meydan C, Foox J, Ramachandran P, Leca J, Lemonnier F, Li WY, Gams MS, Sakamoto T, Chu M, Tobin C, Laugesen E, Robinson TM, You-Ten A, Butler DJ, Berger T, Minden MD, Levine RL, Guidos CJ, Melnick AM, Mason CE, Mak TW. Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells. Proc Natl Acad Sci U S A 2023; 120:e2208176120. [PMID: 36652477 PMCID: PMC9942850 DOI: 10.1073/pnas.2208176120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mutations in IDH1, IDH2, and TET2 are recurrently observed in myeloid neoplasms. IDH1 and IDH2 encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG). Oncogenic IDH1/2 mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include the TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms, IDH1, IDH2, and TET2 mutations may converge on a common oncogenic mechanism. Contrary to this expectation, we observed that they have distinct, and even opposite, effects on hematopoietic stem and progenitor cells in genetically engineered mice. Epigenetic and single-cell transcriptomic analyses revealed that Idh2R172K and Tet2 loss-of-function have divergent consequences on the expression and activity of key hematopoietic and leukemogenic regulators. Notably, chromatin accessibility and transcriptional deregulation in Idh2R172K cells were partially disconnected from DNA methylation alterations. These results highlight unanticipated divergent effects of IDH1/2 and TET2 mutations, providing support for the optimization of genotype-specific therapies.
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Affiliation(s)
- Jerome Fortin
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- 2To whom correspondence may be addressed. , , or
| | - Ming-Feng Chiang
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Cem Meydan
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
- dWorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY10065
| | - Jonathan Foox
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
| | | | - Julie Leca
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - François Lemonnier
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- eInstitut Mondor de Recherche Biomédicale, INSERMU955, Université Paris Est Créteil, Créteil94010, France
| | - Wanda Y. Li
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- fCentre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Miki S. Gams
- gDepartment of Immunology, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ONM5G 0A4, Canada
| | - Takashi Sakamoto
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- hDepartment of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Mandy Chu
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Chantal Tobin
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Eric Laugesen
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Troy M. Robinson
- iHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- jLouis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Annick You-Ten
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Daniel J. Butler
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
| | - Thorsten Berger
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Mark D. Minden
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
| | - Ross L. Levine
- iHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10065
- kCenter for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY10065
- lCenter for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Cynthia J. Guidos
- gDepartment of Immunology, The Hospital for Sick Children Research Institute, University of Toronto, Toronto, ONM5G 0A4, Canada
| | - Ari M. Melnick
- mDepartment of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY10021
| | - Christopher E. Mason
- bDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
- cThe HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY10065
- dWorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY10065
| | - Tak W. Mak
- aPrincess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 2C1, Canada
- fCentre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
- nDepartment of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- 2To whom correspondence may be addressed. , , or
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An Y, Zhao X, Zhang Z, Xia Z, Yang M, Ma L, Zhao Y, Xu G, Du S, Wu X, Zhang S, Hong X, Jin X, Sun K. DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation. Nat Commun 2023; 14:287. [PMID: 36653380 PMCID: PMC9849216 DOI: 10.1038/s41467-023-35959-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Plasma cell-free DNA (cfDNA) are small molecules generated through a non-random fragmentation procedure. Despite commendable translational values in cancer liquid biopsy, however, the biology of cfDNA, especially the principles of cfDNA fragmentation, remains largely elusive. Through orientation-aware analyses of cfDNA fragmentation patterns against the nucleosome structure and integration with multidimensional functional genomics data, here we report a DNA methylation - nuclease preference - cutting end - size distribution axis, demonstrating the role of DNA methylation as a functional molecular regulator of cfDNA fragmentation. Hence, low-level DNA methylation could increase nucleosome accessibility and alter the cutting activities of nucleases during DNA fragmentation, which further leads to variation in cutting sites and size distribution of cfDNA. We further develop a cfDNA ending preference-based metric for cancer diagnosis, whose performance has been validated by multiple pan-cancer datasets. Our work sheds light on the molecular basis of cfDNA fragmentation towards broader applications in cancer liquid biopsy.
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Affiliation(s)
- Yunyun An
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Xin Zhao
- Hepato-Biliary Surgery Division, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Ziteng Zhang
- Hepato-Biliary Surgery Division, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Zhaohua Xia
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Mengqi Yang
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Li Ma
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, 518107, Shenzhen, China
| | - Gang Xu
- Department of Liver Surgery and Liver Transplant Center, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Xiang'an Wu
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Shuowen Zhang
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Xin Hong
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, 518083, Shenzhen, China. .,School of Medicine, South China University of Technology, 510006, Guangzhou, Guangdong, China.
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China.
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Epigenetic Modification of Cytosines in Hematopoietic Differentiation and Malignant Transformation. Int J Mol Sci 2023; 24:ijms24021727. [PMID: 36675240 PMCID: PMC9863985 DOI: 10.3390/ijms24021727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The mammalian DNA methylation landscape is established and maintained by the combined activities of the two key epigenetic modifiers, DNA methyltransferases (DNMT) and Ten-eleven-translocation (TET) enzymes. Once DNMTs produce 5-methylcytosine (5mC), TET proteins fine-tune the DNA methylation status by consecutively oxidizing 5mC to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives. The 5mC and oxidized methylcytosines are essential for the maintenance of cellular identity and function during differentiation. Cytosine modifications with DNMT and TET enzymes exert pleiotropic effects on various aspects of hematopoiesis, including self-renewal of hematopoietic stem/progenitor cells (HSPCs), lineage determination, differentiation, and function. Under pathological conditions, these enzymes are frequently dysregulated, leading to loss of function. In particular, the loss of DNMT3A and TET2 function is conspicuous in diverse hematological disorders, including myeloid and lymphoid malignancies, and causally related to clonal hematopoiesis and malignant transformation. Here, we update recent advances in understanding how the maintenance of DNA methylation homeostasis by DNMT and TET proteins influences normal hematopoiesis and malignant transformation, highlighting the potential impact of DNMT3A and TET2 dysregulation on clonal dominance and evolution of pre-leukemic stem cells to full-blown malignancies. Clarification of the normal and pathological functions of DNA-modifying epigenetic regulators will be crucial to future innovations in epigenetic therapies for treating hematological disorders.
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Müller J, Walter W, Haferlach C, Müller H, Fuhrmann I, Müller ML, Ruge H, Meggendorfer M, Kern W, Haferlach T, Stengel A. How T-lymphoblastic leukemia can be classified based on genetics using standard diagnostic techniques enhanced by whole genome sequencing. Leukemia 2023; 37:217-221. [PMID: 36335263 PMCID: PMC9883150 DOI: 10.1038/s41375-022-01743-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Janine Müller
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wencke Walter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Heiko Müller
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Irene Fuhrmann
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Martha-Lena Müller
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Henning Ruge
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Anna Stengel
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
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Natarajan P. Genomic Aging, Clonal Hematopoiesis, and Cardiovascular Disease. Arterioscler Thromb Vasc Biol 2023; 43:3-14. [PMID: 36353993 PMCID: PMC9780188 DOI: 10.1161/atvbaha.122.318181] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
Chronologic age is the dominant risk factor for coronary artery disease but the features of aging promoting coronary artery disease are poorly understood. Advances in human genetics and population-based genetic profiling of blood cells have uncovered the surprising role of age-related subclinical leukemogenic mutations in blood cells, termed "clonal hematopoiesis of indeterminate potential," in coronary artery disease. Such mutations typically occur in DNMT3A, TET2, ASXL1, and JAK2. Murine and human studies prioritize the role of key inflammatory pathways linking clonal hematopoiesis with coronary artery disease. Increasingly larger, longitudinal, multiomics analyses are enabling further dissection into mechanistic insights. These observations expand the genetic architecture of coronary artery disease, now linking hallmark features of hematologic neoplasia with a much more common cardiovascular condition. Implications of these studies include the prospect of novel precision medicine paradigms for coronary artery disease.
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Affiliation(s)
- Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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48
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Wang X, Liu S, Yu J. Multi-lineage Differentiation from Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:159-175. [PMID: 38228964 DOI: 10.1007/978-981-99-7471-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The hematopoietic stem cells (HSCs) have the ability to differentiate and give rise to all mature blood cells. Commitment to differentiation progressively limits the self-renewal potential of the original HSCs by regulating the level of lineage-specific gene expression. In this review, we will summarize the current understanding of the molecular mechanisms underlying HSC differentiation toward erythroid, myeloid, and lymphocyte lineages. Moreover, we will decipher how the single-cell technologies advance the lineage-biased HSC subpopulations and their differentiation potential.
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Affiliation(s)
- Xiaoshuang Wang
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
| | - Siqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences / Peking Union Medical College, Beijing, China.
- The Institute of Blood Transfusion, Chinese Academy of Medical Sciences / Peking Union Medical College, Chengdu, China.
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49
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Wei A, Wu H. Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. Development 2022; 149:dev182683. [PMID: 36519514 PMCID: PMC10108609 DOI: 10.1242/dev.182683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA methylation is a highly conserved epigenetic modification that plays essential roles in mammalian gene regulation, genome stability and development. Despite being primarily considered a stable and heritable epigenetic silencing mechanism at heterochromatic and repetitive regions, whole genome methylome analysis reveals that DNA methylation can be highly cell-type specific and dynamic within proximal and distal gene regulatory elements during early embryonic development, stem cell differentiation and reprogramming, and tissue maturation. In this Review, we focus on the mechanisms and functions of regulated DNA methylation and demethylation, highlighting how these dynamics, together with crosstalk between DNA methylation and histone modifications at distinct regulatory regions, contribute to mammalian development and tissue maturation. We also discuss how recent technological advances in single-cell and long-read methylome sequencing, along with targeted epigenome-editing, are enabling unprecedented high-resolution and mechanistic dissection of DNA methylome dynamics.
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Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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50
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Xu JJ, Chalk AM, Wall M, Langdon WY, Smeets MF, Walkley CR. Srsf2 P95H/+ co-operates with loss of TET2 to promote myeloid bias and initiate a chronic myelomonocytic leukemia-like disease in mice. Leukemia 2022; 36:2883-2893. [PMID: 36271153 DOI: 10.1038/s41375-022-01727-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
Recurrent mutations in RNA splicing proteins and epigenetic regulators contribute to the development of myelodysplastic syndrome (MDS) and related myeloid neoplasms. In chronic myelomonocytic leukemia (CMML), SRSF2 mutations occur in ~50% of patients and TET2 mutations in ~60%. Clonal analysis indicates that either mutation can arise as the founder lesion. Based on human cancer genetics we crossed an inducible Srsf2P95H/+ mutant model with Tet2fl/fl mice to mutate both concomitantly in hematopoietic stem cells. At 20-24 weeks post mutation induction, we observed subtle differences in the Srsf2/Tet2 mutants compared to either single mutant. Under conditions of native hematopoiesis with aging, we see a distinct myeloid bias and monocytosis in the Srsf2/Tet2 mutants. A subset of the compound Srsf2/Tet2 mutants display an increased granulocytic and distinctive monocytic proliferation (myelomonocytic hyperplasia), with increased immature promonocytes and monoblasts and binucleate promonocytes. Exome analysis of progressed disease demonstrated mutations in genes and pathways similar to those reported in human CMML. Upon transplantation, recipients developed leukocytosis, monocytosis, and splenomegaly. We reproduce Srsf2/Tet2 co-operativity in vivo, yielding a disease with core characteristics of CMML, unlike single Srsf2 or Tet2 mutation. This model represents a significant step toward building high fidelity and genetically tractable models of CMML.
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Affiliation(s)
- Jane Jialu Xu
- St Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia
- Columbia Stem Cell Initiative, Columbia University Irving Medical Centre, New York City, NY, 10032, USA
| | - Alistair M Chalk
- St Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Meaghan Wall
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia
| | - Wallace Y Langdon
- School of Biomedical Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Monique F Smeets
- St Vincent's Institute, Fitzroy, VIC, 3065, Australia.
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia.
| | - Carl R Walkley
- St Vincent's Institute, Fitzroy, VIC, 3065, Australia.
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia.
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